<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/30147?offset=90 https://bioinformaticsonline.com/bookmarks/view/26925/reapr-a-universal-tool-for-genome-assembly-evaluation Wed, 06 Apr 2016 18:26:31 -0500 https://bioinformaticsonline.com/bookmarks/view/26925/reapr-a-universal-tool-for-genome-assembly-evaluation <![CDATA[REAPR: a universal tool for genome assembly evaluation]]> REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.

http://www.sanger.ac.uk/science/tools/reapr

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-5-r47

]]> Jitendra Prajapati https://bioinformaticsonline.com/bookmarks/view/27257/busco-assessing-genome-assembly-and-annotation-completeness-with-benchmarking-universal-single-copy-orthologs Tue, 10 May 2016 07:46:24 -0500 https://bioinformaticsonline.com/bookmarks/view/27257/busco-assessing-genome-assembly-and-annotation-completeness-with-benchmarking-universal-single-copy-orthologs <![CDATA[BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs]]>
  • High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures like N50. 
  • BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. 
  • BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of Benchmarking Universal Single-Copy Orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria. 
  • These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines. 
  • BUSCO assessments offer intuitive metrics, based on evolutionarily informed expectations of gene content from hundreds of species, to gauge completeness of rapidly accumulating genomic data and satisfy an Iberian's quest for quality - "Busco calidad/qualidade".

    • Address of the bookmark: http://busco.ezlab.org/

    ]]>     Anjana     https://bioinformaticsonline.com/bookmarks/view/27328/platanus Fri, 13 May 2016 05:12:40 -0500 https://bioinformaticsonline.com/bookmarks/view/27328/platanus <![CDATA[Platanus]]> Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of
    highly heterozygous diploids from massively parallel shotgun sequencing data.

    The latest version is 1.2.4.

    To cite Platanus, please use the following:

    Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113. [abstract | full text]

    Address of the bookmark: http://platanus.bio.titech.ac.jp/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/30140/cutadapt Wed, 14 Dec 2016 09:59:52 -0600 https://bioinformaticsonline.com/bookmarks/view/30140/cutadapt <![CDATA[Cutadapt]]> Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

    Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

    Cutadapt comes with an extensive suite of automated tests and is available under the terms of the MIT license.

    If you use cutadapt, please cite DOI:10.14806/ej.17.1.200 .

    More at https://github.com/marcelm/cutadapt

    Address of the bookmark: http://cutadapt.readthedocs.io/en/stable/guide.html

    ]]>     Bulbul     https://bioinformaticsonline.com/blog/view/31566/software-and-tools-to-detect-structure-variation-with-long-reads Wed, 15 Mar 2017 14:31:09 -0500 https://bioinformaticsonline.com/blog/view/31566/software-and-tools-to-detect-structure-variation-with-long-reads <![CDATA[Software and Tools to detect structure variation with long reads !!]]> Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs detectable by short-read data.

    With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:

    • Uncover missing heritability linked to structural variation
    • Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
    • Resolve structural variation across the complete size spectrum with basepair resolution

    Following are the SV tools, which can assist you to achieve your goal.

    Sniffles: Structural variation caller using third generation sequencing

    Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled! 

    More at https://github.com/fritzsedlazeck/Sniffles


    MultiBreak-SV:     It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

    There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.

    More at https://github.com/raphael-group/multibreak-sv


    Parliament:     A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?

    Publication about the algorithm and “…the first long-read characterization of structural variation in a diploid human personal genome…” (HS1011) - “Assessing structural variation in a personal genome—towards a human reference diploid genome”

    More at https://sourceforge.net/projects/parliamentsv/

    https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf


    PBHoney: the structural variation discovery tool 

    PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

    Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract

    More at https://sourceforge.net/projects/pb-jelly/


    SMRT-SV:     Structural variant and indel caller for PacBio reads

    Structural variant (SV) and indel caller for PacBio reads based on methods from Chaisson et al. 2014.

    SMRT-SV provides an official software package for tools described in Chaisson et al. 2014 and adds several key features including the following.

    • Unified variant calling user interface with built-in cluster compute support
    • Small indel calling (2-49 bp)
    • Improved inversion calling (screenInversions)
    • Quality metric for SV calls based on number of local assemblies supporting each call
    • Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions
    • Genotyping of SVs with Illumina paired-end reads from WGS samples

    More at https://github.com/EichlerLab/pacbio_variant_caller

    ]]>     Archana Malhotra     https://bioinformaticsonline.com/bookmarks/view/32076/ngs-teaching-material Wed, 05 Apr 2017 04:29:06 -0500 https://bioinformaticsonline.com/bookmarks/view/32076/ngs-teaching-material <![CDATA[NGS teaching material]]> High throughput sequencing (HTS) technologies are being applied to a wide range of important topics in biology. However, the analyses of non-model organisms, for which little previous sequence information is available, pose specific problems. This course addresses the specific strengths and weaknesses of alternative HTS technologies, the computational resources needed for HTS, and how to analyze non-model species using HTS. The course consists of a practical training module, HTS bioinformatics training, and lecturing/seminars of HTS approaches specifically targeting non-model organisms.

    Address of the bookmark: http://marinetics.org/teaching/hts/Assembly.html

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/34475/oxford-nanopore-sequencing-hybrid-error-correction-and-de-novo-assembly-of-a-eukaryotic-genome Wed, 29 Nov 2017 05:08:53 -0600 https://bioinformaticsonline.com/bookmarks/view/34475/oxford-nanopore-sequencing-hybrid-error-correction-and-de-novo-assembly-of-a-eukaryotic-genome <![CDATA[Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome]]> Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

    Address of the bookmark: http://schatzlab.cshl.edu/data/nanocorr/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/35571/medusa-a-multi-draft-based-scaffolder Wed, 14 Feb 2018 02:49:00 -0600 https://bioinformaticsonline.com/bookmarks/view/35571/medusa-a-multi-draft-based-scaffolder <![CDATA[MeDuSa: a multi-draft based scaffolder]]> MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. 

    Address of the bookmark: https://github.com/combogenomics/medusa

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty Tue, 08 May 2018 08:03:21 -0500 https://bioinformaticsonline.com/blog/view/36525/installing-bandage-on-ubunty <![CDATA[Installing Bandage on Ubunty !]]> The following instructions successfully build Bandage (https://github.com/rrwick/Bandage ) on a fresh installation of Ubuntu 14.04:

    1. Ensure the package lists are up-to-date: sudo apt-get update
    2. Install prerequisite packages: sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
    3. Download the Bandage code from GitHub: git clone https://github.com/rrwick/Bandage.git
    4. Open a terminal in the Bandage directory.
    5. Set the environment variable to specify that you will be using Qt 5, not Qt 4: export QT_SELECT=5
    6. Run qmake to generate a Makefile: qmake
    7. Build the program: make
    8. Bandage should now be an executable file.
    9. Optionally, copy the program into /usr/local/bin: sudo make install. The Bandage build directory can then be deleted.

    ➜ Tools git:(master) ✗ sudo apt-get update
    [sudo] password for urbe: 
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    The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A030B21BA07F4FB
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    ➜ Tools git:(master) ✗ sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev
    Reading package lists... Done
    Building dependency tree 
    Reading state information... Done
    build-essential is already the newest version (12.1ubuntu2).
    git is already the newest version (1:2.7.4-0ubuntu1.3).
    The following packages were automatically installed and are no longer required:
    bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic
    linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic linux-signed-image-4.4.0-116-generic runc ubuntu-fan
    Use 'sudo apt autoremove' to remove them.
    The following additional packages will be installed:
    libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5
    libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5test5 libqt5widgets5 libqt5xml5 libwayland-bin
    libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0 libxcb-render0-dev
    libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev qt5-qmake
    qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev
    Suggested packages:
    libqt5libqgtk2 qt5-image-formats-plugins qtwayland5 libxext-doc libmysqlclient-dev libpq-dev libsqlite3-dev unixodbc-dev
    The following NEW packages will be installed:
    libdrm-dev libegl1-mesa-dev libgl1-mesa-dev libgles2-mesa libgles2-mesa-dev libglu1-mesa-dev libmirclient-dev libmircommon-dev libmircookie-dev libmircookie2 libmircore-dev libprotobuf-dev libprotobuf9v5
    libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5printsupport5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5svg5-dev libqt5test5 libqt5widgets5 libqt5xml5
    libwayland-bin libwayland-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render-util0
    libxcb-render0-dev libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xkb1 libxdamage-dev libxext-dev libxfixes-dev libxkbcommon-dev libxkbcommon-x11-0 libxshmfence-dev libxxf86vm-dev mesa-common-dev
    qt5-qmake qtbase5-dev qtbase5-dev-tools qttranslations5-l10n x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-xext-dev x11proto-xf86vidmode-dev
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    Get:43 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircommon-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [14,9 kB]
    Get:44 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie2 amd64 0.26.3+16.04.20170605-0ubuntu1.1 [22,5 kB]
    Get:45 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmircookie-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [5.152 B]
    Get:46 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libmirclient-dev amd64 0.26.3+16.04.20170605-0ubuntu1.1 [42,6 kB]
    Get:47 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libegl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [19,9 kB]
    Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa amd64 17.2.8-0ubuntu0~16.04.1 [13,4 kB]
    Get:49 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgles2-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [40,2 kB]
    Get:50 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 mesa-common-dev amd64 17.2.8-0ubuntu0~16.04.1 [525 kB]
    Get:51 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgl1-mesa-dev amd64 17.2.8-0ubuntu0~16.04.1 [4.456 B]
    Get:52 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1 [202 kB]
    Get:53 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5concurrent5 amd64 5.5.1+dfsg-16ubuntu7.5 [24,3 kB]
    Get:54 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5 amd64 5.5.1+dfsg-16ubuntu7.5 [128 kB]
    Get:55 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5printsupport5 amd64 5.5.1+dfsg-16ubuntu7.5 [174 kB]
    Get:56 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5 amd64 5.5.1+dfsg-16ubuntu7.5 [104 kB]
    Get:57 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5test5 amd64 5.5.1+dfsg-16ubuntu7.5 [84,5 kB]
    Get:58 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5xml5 amd64 5.5.1+dfsg-16ubuntu7.5 [91,8 kB]
    Get:59 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qt5-qmake amd64 5.5.1+dfsg-16ubuntu7.5 [1.192 kB]
    Get:60 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev-tools amd64 5.5.1+dfsg-16ubuntu7.5 [1.056 kB]
    Get:61 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 qtbase5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [931 kB]
    Get:62 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5opengl5-dev amd64 5.5.1+dfsg-16ubuntu7.5 [31,5 kB]
    Get:63 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libqt5sql5-sqlite amd64 5.5.1+dfsg-16ubuntu7.5 [33,0 kB]
    Get:64 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 qttranslations5-l10n all 5.5.1-2build1 [1.210 kB]
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    Setting up libmirclient-dev:amd64 (0.26.3+16.04.20170605-0ubuntu1.1) ...
    Setting up libegl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libgles2-mesa:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libgles2-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up mesa-common-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libgl1-mesa-dev:amd64 (17.2.8-0ubuntu0~16.04.1) ...
    Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1) ...
    Setting up libqt5concurrent5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5opengl5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5printsupport5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5sql5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5test5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5xml5:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qt5-qmake:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qtbase5-dev-tools (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qtbase5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5opengl5-dev:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up libqt5sql5-sqlite:amd64 (5.5.1+dfsg-16ubuntu7.5) ...
    Setting up qttranslations5-l10n (5.5.1-2build1) ...
    Processing triggers for libc-bin (2.23-0ubuntu10) ...
    ➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Bandage.git
    Cloning into 'Bandage'...
    remote: Counting objects: 7813, done.
    remote: Total 7813 (delta 0), reused 0 (delta 0), pack-reused 7813
    Receiving objects: 100% (7813/7813), 27.43 MiB | 16.33 MiB/s, done.
    Resolving deltas: 100% (5973/5973), done.
    Checking connectivity... done.
    ➜ Tools git:(master) ✗ cd Bandage 
    ➜ Bandage git:(master) ls
    Bandage.pro BandageTests.pro blast build_scripts command_line COPYING graph images ogdf program README.md tests ui
    ➜ Bandage git:(master) export QT_SELECT=5
    ➜ Bandage git:(master) qmake
    ➜ Bandage git:(master) ✗ make
    /home/urbe/anaconda3/bin/uic ui/mainwindow.ui -o ui_mainwindow.h
    /home/urbe/anaconda3/bin/uic ui/settingsdialog.ui -o ui_settingsdialog.h
    /home/urbe/anaconda3/bin/uic ui/aboutdialog.ui -o ui_aboutdialog.h
    /home/urbe/anaconda3/bin/uic ui/enteroneblastquerydialog.ui -o ui_enteroneblastquerydialog.h
    /home/urbe/anaconda3/bin/uic ui/blastsearchdialog.ui -o ui_blastsearchdialog.h
    /home/urbe/anaconda3/bin/uic ui/myprogressdialog.ui -o ui_myprogressdialog.h
    /home/urbe/anaconda3/bin/uic ui/pathspecifydialog.ui -o ui_pathspecifydialog.h
    /home/urbe/anaconda3/bin/uic ui/querypathsdialog.ui -o ui_querypathsdialog.h
    /home/urbe/anaconda3/bin/uic ui/blasthitfiltersdialog.ui -o ui_blasthitfiltersdialog.h
    /home/urbe/anaconda3/bin/uic ui/changenodenamedialog.ui -o ui_changenodenamedialog.h
    /home/urbe/anaconda3/bin/uic ui/graphinfodialog.ui -o ui_graphinfodialog.h
    /home/urbe/anaconda3/bin/uic ui/changenodedepthdialog.ui -o ui_changenodedepthdialog.h
    g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o main.o program/main.cpp
    g++ -c -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -I. -Iui -I/usr/include -I../../anaconda3/include/qt -I../../anaconda3/include/qt/QtSvg -I../../anaconda3/include/qt/QtWidgets -I../../anaconda3/include/qt/QtGui -I../../anaconda3/include/qt/QtCore -I. -I. -I../../anaconda3/mkspecs/linux-g++ -o settings.o program/settings.cpp
    ....

    ...
    g++ -Wl,-O1 -Wl,-rpath,/home/urbe/anaconda3/lib -o Bandage main.o settings.o globals.o graphlayoutworker.o debruijnnode.o debruijnedge.o graphicsitemnode.o graphicsitemedge.o mainwindow.o graphicsviewzoom.o settingsdialog.o mygraphicsview.o mygraphicsscene.o aboutdialog.o enteroneblastquerydialog.o blasthit.o blastqueries.o blastsearchdialog.o infotextwidget.o assemblygraph.o verticalscrollarea.o myprogressdialog.o nodewidthvisualaid.o verticallabel.o load.o image.o commoncommandlinefunctions.o mytablewidget.o buildblastdatabaseworker.o colourbutton.o blastquery.o runblastsearchworker.o blastsearch.o path.o pathspecifydialog.o graphlocation.o tablewidgetitemint.o tablewidgetitemdouble.o tablewidgetitemshown.o memory.o querypathspushbutton.o querypathsdialog.o blastquerypath.o blasthitfiltersdialog.o scinot.o changenodenamedialog.o querypathsequencecopybutton.o querypaths.o info.o reduce.o Graph.o GraphAttributes.o FMMMLayout.o geometry.o ClusterGraphAttributes.o FruchtermanReingold.o NMM.o GmlParser.o simple_graph_alg.o basic.o XmlParser.o String.o Hashing.o PoolMemoryAllocator.o GraphCopy.o CombinatorialEmbedding.o OgmlParser.o ClusterGraph.o Math.o EdgeAttributes.o NodeAttributes.o MAARPacking.o Multilevel.o numexcept.o Set.o Ogml.o DinoXmlParser.o DinoXmlScanner.o DinoTools.o DinoLineBuffer.o System.o QuadTreeNM.o QuadTreeNodeNM.o Constraint.o MultilevelGraph.o graphinfodialog.o tablewidgetitemname.o changenodedepthdialog.o qrc_images.o moc_graphlayoutworker.o moc_mainwindow.o moc_graphicsviewzoom.o moc_settingsdialog.o moc_mygraphicsview.o moc_mygraphicsscene.o moc_aboutdialog.o moc_enteroneblastquerydialog.o moc_blastquery.o moc_blastsearchdialog.o moc_infotextwidget.o moc_assemblygraph.o moc_verticalscrollarea.o moc_myprogressdialog.o moc_nodewidthvisualaid.o moc_verticallabel.o moc_mytablewidget.o moc_buildblastdatabaseworker.o moc_colourbutton.o moc_runblastsearchworker.o moc_pathspecifydialog.o moc_querypathspushbutton.o moc_querypathsdialog.o moc_blasthitfiltersdialog.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.o moc_graphinfodialog.o moc_changenodedepthdialog.o -L/usr/lib -L/home/urbe/anaconda3/lib -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread 
    ➜ Bandage git:(master) ✗ ls 
    aboutdialog.o DinoTools.o Makefile moc_infotextwidget.cpp moc_verticalscrollarea.o scinot.o
    assemblygraph.o DinoXmlParser.o Math.o moc_infotextwidget.o MultilevelGraph.o Set.o
    Bandage DinoXmlScanner.o memory.o moc_mainwindow.cpp Multilevel.o settingsdialog.o
    Bandage.pro EdgeAttributes.o moc_aboutdialog.cpp moc_mainwindow.o mygraphicsscene.o settings.o
    BandageTests.pro enteroneblastquerydialog.o moc_aboutdialog.o moc_mygraphicsscene.cpp mygraphicsview.o simple_graph_alg.o
    basic.o FMMMLayout.o moc_assemblygraph.cpp moc_mygraphicsscene.o myprogressdialog.o String.o
    blast FruchtermanReingold.o moc_assemblygraph.o moc_mygraphicsview.cpp mytablewidget.o System.o
    blasthitfiltersdialog.o geometry.o moc_blasthitfiltersdialog.cpp moc_mygraphicsview.o NMM.o tablewidgetitemdouble.o
    blasthit.o globals.o moc_blasthitfiltersdialog.o moc_myprogressdialog.cpp NodeAttributes.o tablewidgetitemint.o
    blastqueries.o GmlParser.o moc_blastquery.cpp moc_myprogressdialog.o nodewidthvisualaid.o tablewidgetitemname.o
    blastquery.o graph moc_blastquery.o moc_mytablewidget.cpp numexcept.o tablewidgetitemshown.o
    blastquerypath.o GraphAttributes.o moc_blastsearchdialog.cpp moc_mytablewidget.o ogdf tests
    blastsearchdialog.o GraphCopy.o moc_blastsearchdialog.o moc_nodewidthvisualaid.cpp Ogml.o ui
    blastsearch.o graphicsitemedge.o moc_buildblastdatabaseworker.cpp moc_nodewidthvisualaid.o OgmlParser.o ui_aboutdialog.h
    buildblastdatabaseworker.o graphicsitemnode.o moc_buildblastdatabaseworker.o moc_pathspecifydialog.cpp path.o ui_blasthitfiltersdialog.h
    build_scripts graphicsviewzoom.o moc_changenodedepthdialog.cpp moc_pathspecifydialog.o pathspecifydialog.o ui_blastsearchdialog.h
    changenodedepthdialog.o graphinfodialog.o moc_changenodedepthdialog.o moc_querypathsdialog.cpp PoolMemoryAllocator.o ui_changenodedepthdialog.h
    changenodenamedialog.o graphlayoutworker.o moc_changenodenamedialog.cpp moc_querypathsdialog.o program ui_changenodenamedialog.h
    ClusterGraphAttributes.o graphlocation.o moc_changenodenamedialog.o moc_querypathsequencecopybutton.cpp qrc_images.cpp ui_enteroneblastquerydialog.h
    ClusterGraph.o Graph.o moc_colourbutton.cpp moc_querypathsequencecopybutton.o qrc_images.o ui_graphinfodialog.h
    colourbutton.o Hashing.o moc_colourbutton.o moc_querypathspushbutton.cpp QuadTreeNM.o ui_mainwindow.h
    CombinatorialEmbedding.o image.o moc_enteroneblastquerydialog.cpp moc_querypathspushbutton.o QuadTreeNodeNM.o ui_myprogressdialog.h
    command_line images moc_enteroneblastquerydialog.o moc_runblastsearchworker.cpp querypathsdialog.o ui_pathspecifydialog.h
    commoncommandlinefunctions.o info.o moc_graphicsviewzoom.cpp moc_runblastsearchworker.o querypathsequencecopybutton.o ui_querypathsdialog.h
    Constraint.o infotextwidget.o moc_graphicsviewzoom.o moc_settingsdialog.cpp querypaths.o ui_settingsdialog.h
    COPYING load.o moc_graphinfodialog.cpp moc_settingsdialog.o querypathspushbutton.o verticallabel.o
    debruijnedge.o MAARPacking.o moc_graphinfodialog.o moc_verticallabel.cpp README.md verticalscrollarea.o
    debruijnnode.o main.o moc_graphlayoutworker.cpp moc_verticallabel.o reduce.o XmlParser.o
    DinoLineBuffer.o mainwindow.o moc_graphlayoutworker.o moc_verticalscrollarea.cpp runblastsearchworker.o
    ➜ Bandage git:(master) ✗ ./Bandage

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/36723/hapsembler-an-assembler-for-highly-polymorphic-genomes Tue, 22 May 2018 04:09:53 -0500 https://bioinformaticsonline.com/bookmarks/view/36723/hapsembler-an-assembler-for-highly-polymorphic-genomes <![CDATA[Hapsembler: An Assembler for Highly Polymorphic Genomes]]> Address of the bookmark: http://compbio.cs.toronto.edu/hapsembler/

    ]]>     Jit